How to create eyeballs holes without messing up the mesh and the topology?
You need to create more mesh lines around the eyes in order for there to be more points that Blender can use to maintain the form. Each vertex is a point on the mesh that Blender uses to calculate the surface area, so if you have too few vertices, it can only calculate the shape based on those few points. Add more mesh lines and use the vertices on them to give Blender more points to work with. 

There are many ways to add more mesh. Listing them here is not possible. Play around with the various mesh tools and consult the documents for explanations on how to use them.